Research Software Engineer - Collaborative Open Omics (COPO)
Post Details
Job Title
Research Software Engineer - Collaborative Open Omics (COPO)
Post Number
1004290
Closing Date
12 Oct 2022
Grade
SC5
Starting Salary
£42,050 - £51,950
Hours per week
37
Months Duration
36

Job Description

Main Purpose of the Job

Applications are invited for a Research Software Engineer - Collaborative Open Omics (COPO) to join the Laboratory of Dr Robert Davey in the Digital Biology Programme at the Earlham Institute.

Working in a professional team of Research Software Engineers, the role will be tasked with supporting the development and maintenance the “Collaborative OPen Omics” (COPO) platform, which is a data and metadata brokering service for national and international communities such as Darwin Tree of Life and the European Reference Genome Atlas. COPO helps life science researchers to implement data and metadata management practices to submit research outputs to public repositories.
The post holder will:
• Continue to develop COPO to become a single point-of-access for end users, and a range of web services via APIs, that enable scientists to attribute metadata, deposit data into public repositories, ascribe accessions to these data, and link them with associated publications.
• Manage the strategic development and delivery of high-quality software solutions that provide essential tracking and lifecycle processing of data managed by the COPO platform.
• Devise and implement novel approaches to improve large-scale data description, deposition tools, and access across the UK and international life science research community.
• Contribute to, promote, and implement FAIR standards for open informatics in the biosciences.
• Engage with life scientists by attending national and international meetings to promote data management and related infrastructure, and by providing training on the COPO platform.

Key Relationships

Internal: Reporting to the lead Research Software Engineer with a key role to play in the development and delivery of the COPO infrastructure. Working with the EI (Earlham Institute) Capabilities in Genomics, e-Infrastructure and Training to support data management, develop materials, and deliver training on the COPO platform.
Managing: No immediate management responsibilities.
Interacting with: All EI staff.
External: Data curators at key projects such as Darwin Tree of Life, European Genome Reference Atlas and Earth Biogenome Project, data repositories at the European Bioinformatics Institute (EBI); representatives of the UK and international bioscience community; UK and international data management scientists; API and service providers for data and analysis management services such as CyVerse and CyVerse UK, Galaxy, CKAN, figshare, etc.

Main Activities & Responsibilities

Percentage
To work with colleagues in the group to develop COPO, as well as EI’s tools for data and metadata management that are guided by strategic needs and technological advances.
Reduce the burden of data management for researchers, enabling them to share their data and results more effectively by establishing interoperability solutions between a range of existing data services.
To establish associated best practice guidelines for bioscience data management, interoperability, and publication strategies.
75
To network widely with academic and industrial groups on the Norwich Research Park, throughout the UK and internationally, including the Darwin Tree of Life, European Biogenome Atlas projects, the European Bioinformatics Institute, ELIXIR, other genomics facilities nationally and internationally, and with bioinformaticians globally, such as the CyVerse and Galaxy efforts.
10
To communicate the work of EI in oral and written presentations and to publish novel technological developments in scientific journals.
10
To provide an efficient and cost-effective data management platform to exploit EI’s hardware and software expertise, promoting EI as a National Capability for UK bioscience.
5
As agreed with line manager, any other duties commensurate with the nature of the role

Person Profile

Education & Qualifications

Requirement
Importance
BSc, equivalent professional qualification, or convincing evidence of practical role in a suitable area of computer science or software development
Essential
MSc and/or PhD in a relevant subject, e.g., computer science, bioinformatics
Desirable

Specialist Knowledge & Skills

Requirement
Importance
Up to date knowledge and experience of Python 3, with a focus on Django or similar web framework
Essential
Experience of the JavaScript programming language and some associated libraries
Essential
Working knowledge and experience with MongoDB NoSQL database management systems
Desirable
Experience of Cloud architectures and Docker
Desirable
Knowledge of ontologies
Desirable

Relevant Experience

Requirement
Importance
Experience of working in a rapidly changing technological environment
Essential
Ability to manage one’s own time and priorities, excepting operational necessities
Essential
Interest in open-source
Essential
Experience in data management and metadata attribution
Desirable
Experience in open-source software engineering and associated tools
Desirable

Interpersonal & Communication Skills

Requirement
Importance
Excellent communication skills, both written and verbal
Essential
To be able to communicate clearly with EI staff at all levels across research disciplines and technical expertise levels
Essential
Good interpersonal skills, with the ability to work well as part of a team
Essential
Interest in creating functional user experiences, and interconnected software systems using APIs
Desirable

Additional Requirements

Requirement
Importance
Attention to detail
Essential
Promotes equality and values diversity
Essential
Willingness to work outside standard working hours when required
Essential
Able to present a positive image of self and the Institute, promoting both the international reputation and public engagement aims of the Institute
Essential
Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to work
Essential
Ability to maintain confidentiality and security of information where appropriate
Essential

Who We Are

Earlham Institute

Earlham Institute is a vibrant, contemporary research institute and registered charity, working in an area of rapid technological development and innovation.

Earlham Institute is strategically funded by the BBSRC to lead the development of a skill base in bioinformatics and a genomics technology platform for UK bioscience. The Institute is located on the Norwich Research Park, together with its partners: the John Innes Centre, the Institute of Food Research, The Sainsbury Laboratory, the University of East Anglia and the Norfolk and Norwich University Hospital. The research park has an excellent reputation for research in plant and microbial sciences, interdisciplinary environmental science and food, diet and health, to which Earlham Institute contributes strengths in genomics and bioinformatics. Close links exist between the NRP partners and new opportunities for collaboration in exciting new initiatives are under development. The NRP recently received £26M of government investment to facilitate innovation and further develop infrastructure to attract science and technology companies to the Park to enhance the vibrant environment and realise economic impact from research investment.

Earlham Institute is a UK hub for innovative Bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. This has been boosted recently by an e-Infrastructure grant to expand the data storage capacity to a multi-petabyte unit, deploying a high performance cluster and large-memory server enabling the allocation of processes requiring several terabytes of computing memory.

Earlham Institute’s state of the art DNA sequencing facility operates multiple complementary technologies for data generation that provide the foundation for analyses furthering our fundamental understanding of genomes and how they function. We aim to be at the forefront of technological advances and are developing and implementing technologies to generate and analyse new types of data. We also develop novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational bioscience. Earlham Institute has one fully owned subsidiary, Genome Enterprise Ltd (GEL) via which it offers genomic and bioinformatics services on a trading basis and works with commercial providers on a partnership basis. Earlham Institute also receives specific funding to enable knowledge exchange programmes which are supported across the institute teams.

Department

Digital Biology

Group Details

The Davey group works on a range of infrastructure, HPC and software projects to enhance the biosciences in terms of data management, interoperability, open science, metadata collection curation and validation, data brokering, and AI data annotation.

Living in Norfolk

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Research Software Engineer - Collaborative Open Omics (COPO)

Applications are invited for a Research Software Engineer - Collaborative Open Omics (COPO) to join the Laboratory of Dr Robert Davey in the Digital Biology Programme at the Earlham Institute, based in Norwich, UK.

Background:

The post will continue the development of the BBSRC-funded project, “Collaborative Open Omics (COPO): a community-guided platform for plant science” (BB/L024055/1). Whilst COPO was originally developed for plant scientists, we have extended its reach to other life science domains. As such, COPO helps life science researchers to implement data and metadata management practices to submit research outputs to public repositories. COPO has helped broker metadata for tens of thousands of samples and datafiles to date and is entering a new period of growth. 

COPO has been used for EI’s own strategic data management implementation, as well as being a key component of the Darwin Tree of Life project, having handled metadata for over 40,000 species. Therefore, this is an exciting role with international collaborators and a global reach.

The post holder will develop potentially ground-breaking advances to improve the access and understanding of data deposition and dissemination services to enable the life science research community to manage and publicise their data effectively. 
A push for open data in this community will benefit internal researchers, external collaborators, and the global bioinformatics community.

EI is a UK hub for innovative bioinformatics and genomics approaches tied to extensive local compute infrastructure, and their combined applications in a broad spectrum of UK bioscience.  

The role:

The post holder will:

•Continue to develop COPO to become a single point-of-access for end users, and a range of web services via APIs, that enable scientists to attribute metadata, deposit data into public repositories, ascribe accessions to these data, and link them with associated publications.
•Manage the strategic development and delivery of high-quality software solutions that provide essential tracking and lifecycle processing of data managed by the COPO platform.
•Devise and implement novel approaches to improve large-scale data description, deposition tools, and access across the UK and international life science research community.
•Contribute to, promote, and implement FAIR standards for open informatics in the biosciences.
•Engage with life scientists by attending national and international meetings to promote data management and related infrastructure, and by providing training on the COPO platform.

The ideal candidate:

The ideal candidate will have up to date knowledge and experience of Python 3, with a focus on Django or similar web framework and experience of the JavaScript programming language and some associated libraries. Working knowledge and experience with MongoDB NoSQL database management systems and experience of Cloud architectures and Docker are desirable.

Additional information:

Salary on appointment will be within the range £42,050 to £51,950 per annum depending on qualifications and experience.  This is a full-time post for a contract of 3 years.

As a Disability Confident employer, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy.

The closing date for applications will be 12th October 2022.